A new method may make it easier to ferret out the health impacts of different bacteria in the intestines. The work could lead to new probiotics, microorganisms that may provide health benefits when consumed, and has already identified a handful of microbes that may contribute to obesity.

Scientists have discovered many links between human health and particular mixes of microbes that live in and on the body. But it hasn’t been easy to pin a health effect on one or a few of the hundreds of diff...